• using R Under development (unstable) (2026-10-15 r90674)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.3     flang version 23.1.3
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-10-15 13:38:53 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘scNPM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘scNPM’ version ‘1.0.6’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘scNPM’ can be installed ... [30s/25s] OK See the install log for details.
• used C++ compiler: ‘clang version 23.1.3’
• checking C++ specification ... INFO   specified C++17
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [12s/12s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... ERROR   Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(scNPM)   >   > test_check("scNPM")   OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.   OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).   Saving _problems/test-staged-fdr-158.R   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 537 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-staged-fdr.R:158:5'): invalid stage budgets and insufficient stability cannot produce discoveries ──   Expected `staged_run(a)` to throw a error.   Backtrace:       ▆    1. ├─scNPM (local) staged_single_thread(...) at test-staged-fdr.R:156:3    2. │ └─base::force(code) at test-staged-fdr.R:3:47    3. └─testthat::expect_error(staged_run(a), "Matching did not stabilize") at test-staged-fdr.R:158:5      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 537 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR